Thanks for the response. I have made a lot of progress since posting my message.

A kind soul gave me some tips. I was using mot files plus init,c, and he told me that was not necessary, so I ditched the mot files. He also told me I needed an init.c that was written for the Kstep, so I dug out InitKstep3Axis and modified it for two axes. Now the lathe functions in both Mach3 and KMotionCNC.

He suggested I choose higher jerk figures, but I don't know what the right figures would be. The software chose 4+e006 all by itself.

I am having problems with the lathe losing steps. It looks like the steps/inch on the x axis works best at 81540, and on z I'm getting 6475, but these don't match the calculations for a 25 TPI screw and 8 TPI screw. The guy who helped me suggested lower speeds and accelerations, but I'm not sure what's appropriate for a mini-lathe. It's not like I'm doing production, so I don't need much speed.

He also said I should change the code so the amps don't shut off. Something about losing the tool position.

Anyway, here is the code.

#include "KMotionDef.h"

// Defines axis 0, 1 as simple step dir TTL outputs for KSTEP
// enables them
// sets them as an xz coordinate system for GCode

int main()
{
    double T0, LastX=0, LastZ=0, Tau;
   
    KStepPresent=TRUE;      // enable KSTEP input multiplexing
    FPGA(KAN_TRIG_REG)=4;      // Mux PWM0 to JP7 Pin5 IO 44 for KSTEP

    FPGA(STEP_PULSE_LENGTH_ADD) = 63 + 0x80;  // set polarity and pulse length to 4us
   
    ch0->InputMode=NO_INPUT_MODE;
    ch0->OutputMode=STEP_DIR_MODE;
    ch0->Vel=40000;
    ch0->Accel=200000;
    ch0->Jerk=4e+006;
    ch0->P=0;
    ch0->I=0.01;
    ch0->D=0;
    ch0->FFAccel=0;
    ch0->FFVel=0;
    ch0->MaxI=200;
    ch0->MaxErr=1e+006;
    ch0->MaxOutput=200;
    ch0->DeadBandGain=1;
    ch0->DeadBandRange=0;
    ch0->InputChan0=0;
    ch0->InputChan1=0;
    ch0->OutputChan0=8;
    ch0->OutputChan1=0;
    ch0->MasterAxis=-1;
    ch0->LimitSwitchOptions=0x0;
    ch0->SoftLimitPos=1e+030;
    ch0->SoftLimitNeg=-1e+030;
    ch0->InputGain0=1;
    ch0->InputGain1=1;
    ch0->InputOffset0=0;
    ch0->InputOffset1=0;
    ch0->OutputGain=1;
    ch0->OutputOffset=0;
    ch0->SlaveGain=1;
    ch0->BacklashMode=BACKLASH_OFF;
    ch0->BacklashAmount=0;
    ch0->BacklashRate=0;
    ch0->invDistPerCycle=1;
    ch0->Lead=0;
    ch0->MaxFollowingError=1000000000;
    ch0->StepperAmplitude=20;

    ch0->iir[0].B0=1;
    ch0->iir[0].B1=0;
    ch0->iir[0].B2=0;
    ch0->iir[0].A1=0;
    ch0->iir[0].A2=0;

    ch0->iir[1].B0=1;
    ch0->iir[1].B1=0;
    ch0->iir[1].B2=0;
    ch0->iir[1].A1=0;
    ch0->iir[1].A2=0;

    ch0->iir[2].B0=0.000769;
    ch0->iir[2].B1=0.001538;
    ch0->iir[2].B2=0.000769;
    ch0->iir[2].A1=1.92076;
    ch0->iir[2].A2=-0.923833;
    EnableAxisDest(0,0);

    ch1->InputMode=NO_INPUT_MODE;
    ch1->OutputMode=STEP_DIR_MODE;
    ch1->Vel=40000;
    ch1->Accel=200000;
    ch1->Jerk=4e+006;
    ch1->P=0;
    ch1->I=0.01;
    ch1->D=0;
    ch1->FFAccel=0;
    ch1->FFVel=0;
    ch1->MaxI=200;
    ch1->MaxErr=1e+006;
    ch1->MaxOutput=200;
    ch1->DeadBandGain=1;
    ch1->DeadBandRange=0;
    ch1->InputChan0=0;
    ch1->InputChan1=0;
    ch1->OutputChan0=9;
    ch1->OutputChan1=0;
    ch1->MasterAxis=-1;
    ch1->LimitSwitchOptions=0x0;
    ch1->SoftLimitPos=1e+030;
    ch1->SoftLimitNeg=-1e+030;
    ch1->InputGain0=1;
    ch1->InputGain1=1;
    ch1->InputOffset0=0;
    ch1->InputOffset1=0;
    ch1->OutputGain=1;
    ch1->OutputOffset=0;
    ch1->SlaveGain=1;
    ch1->BacklashMode=BACKLASH_OFF;
    ch1->BacklashAmount=0;
    ch1->BacklashRate=0;
    ch1->invDistPerCycle=1;
    ch1->Lead=0;
    ch1->MaxFollowingError=1000000000;
    ch1->StepperAmplitude=20;

    ch1->iir[0].B0=1;
    ch1->iir[0].B1=0;
    ch1->iir[0].B2=0;
    ch1->iir[0].A1=0;
    ch1->iir[0].A2=0;

    ch1->iir[1].B0=1;
    ch1->iir[1].B1=0;
    ch1->iir[1].B2=0;
    ch1->iir[1].A1=0;
    ch1->iir[1].A2=0;

    ch1->iir[2].B0=0.000769;
    ch1->iir[2].B1=0.001538;
    ch1->iir[2].B2=0.000769;
    ch1->iir[2].A1=1.92076;
    ch1->iir[2].A2=-0.923833;
    EnableAxisDest(1,0);

   

    DefineCoordSystem(0,-1,1,-1);
   
    SetBitDirection(45,1);  // set Enable Signal as Output
    SetBit(45);                // Enable the amplifiers
   
//  Add a small amount of Coordinated Motion Path smoothing if desired
//    Tau = 0.001;  // seconds for Low Pass Filter Time Constant
//    KLP = exp(-TIMEBASE/Tau);
    KLP=0; // force to 0 to disable
//    printf("Tau=%f KLP=%f\n",Tau,KLP);
   
   
    for (;;) // loop forever
    {
        WaitNextTimeSlice();
       
        // Service Amplifier disable after no activity for a while
        if (ch0->Dest != LastX || ch1->Dest != LastZ)
        {
            // we moved - enable KStep Amplifers
            SetBit(45);
            T0 = Time_sec();  // record the time and position of last motion
            LastX=ch0->Dest;
            LastZ=ch1->Dest;
        }
        else
        {
            if (Time_sec() > T0 + 10.0) ClearBit(45);
        }
    }

    return 0;
}

I should also add that now the axes are running backward again. Mach3 won't fix it, but I made it work by switching the output gain values in KMotion. The "State" boxes on lines 2 and 3 on the Digital Output screen are blinking.